› 8ghu

Electron Microscopy
3Å resolution

Methyltransferase RmtC bound to the 30S ribosomal subunit

Released:
DOI: 10.2210/pdb8ghu/pdb
PDB entry 8ghu coloured by chain, front view.
PDB entry 8ghu coloured by chain, side view.
PDB entry 8ghu coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC.
Srinivas P, Nosrati M, Zelinskaya N, Dey D, Comstock LR, Dunham CM, Conn GL
OpenAccess logo bioRxiv (2023)
PMID: 36993224
Related structures: EMD-40051

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + guanine(1405) in 16S rRNA = S-adenosyl-L-homocysteine + N(7)-methylguanine(1405) in 16S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
PDBe Complex ID:
PDB-CPX-229001 (preferred)
Entry contents:
14 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (15 distinct):
16S rRNA (guanine(1405)-N(7))-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 281 amino acids
Theoretical weight: 32.15 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: G4WZ44 (Residues: 15-295; Coverage: 95%)
Gene names: pNDM102337_133, rmtC
Sequence domains: Ribosomal RNA methyltransferase (FmrO)
Small ribosomal subunit protein uS3 Chain: c
Molecule details ›
Chain: c
Length: 206 amino acids
Theoretical weight: 23.08 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V3 (Residues: 2-207; Coverage: 88%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: d
Molecule details ›
Chain: d
Length: 205 amino acids
Theoretical weight: 23.38 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V8 (Residues: 2-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: e
Molecule details ›
Chain: e
Length: 150 amino acids
Theoretical weight: 15.8 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W1 (Residues: 10-159; Coverage: 90%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6, non-modified isoform Chain: f
Molecule details ›
Chain: f
Length: 100 amino acids
Theoretical weight: 11.67 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02358 (Residues: 1-100; Coverage: 74%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: g
Molecule details ›
Chain: g
Length: 151 amino acids
Theoretical weight: 16.86 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02359 (Residues: 2-152; Coverage: 84%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: h
Molecule details ›
Chain: h
Length: 129 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W7 (Residues: 2-130; Coverage: 99%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 123 amino acids
Theoretical weight: 13.64 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S3 (Residues: 2-124; Coverage: 99%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: m
Molecule details ›
Chain: m
Length: 93 amino acids
Theoretical weight: 10.36 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S9 (Residues: 2-94; Coverage: 79%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 88 amino acids
Theoretical weight: 10.16 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADZ4 (Residues: 2-89; Coverage: 99%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: q
Molecule details ›
Chain: q
Length: 80 amino acids
Theoretical weight: 9.26 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG63 (Residues: 4-83; Coverage: 95%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: r
Molecule details ›
Chain: r
Length: 55 amino acids
Theoretical weight: 6.47 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T7 (Residues: 20-74; Coverage: 73%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 85 amino acids
Theoretical weight: 9.51 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U7 (Residues: 3-87; Coverage: 98%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1532 nucleotides
Theoretical weight: 496.97 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand MG 83 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-40051
Expression system: Escherichia coli

Quick links

Citations

2 mentions without citation

30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC.
Srinivas et al. (2023)
1 more